I am a researcher in origins of life, a field that deals with hypotheses about evolutionary processes that took place before LUCA (the last universal common ancestor), and with the chemical processes that gave rise to life and evolution in the first place. This is very hard to study empirically, and as a consequence there are many competing hypotheses. However, I've noticed that many of them have a common form, which I will describe below. My question is about whether hypotheses of this particular form exist (and have been investigated, for example using phylogenetic methods) in post-LUCA evolutionary biology.
My reason for asking is that my colleagues and I were not able to think of a good example. If no example is known in post-LUCA evolutionary biology then it casts doubt on the plausibility of this type of hypothesis in pre-LUCA evolution. I suspect this is the case, and therefore my ideal answer would provide me with bibliographic material to support a claim that there just aren't any good examples of this in evolutionary biology. However, I would also be happy to be proven wrong with a really good example.
Hypotheses regarding the origins of life are difficult to test empirically, because phylogenetic methods can give us little direct evidence about anything before LUCA, and because there are no fossils dating from that time. (The entirety of Earth's surface has since been replaced by plate tectonics.) Consequently there are a number of competing hypotheses that differ from one another in almost every way. However, I've noticed that many of them have a common form: they say that
one or more of the features of a modern (i.e. post-LUCA) cell were originally provided by an external mechanism, in the form of abiotic chemical processes that took place in some very specific microenvironment, and
evolution eventually provided a solution that very closely echoed the one that had originally been provided by the environment.
Point (1) seems relatively easy to satisfy in an evolutionary scenario; it's point (2) that I'm specifically interested in. The two most popular hypotheses in the field both have this form:
Some forms of the The RNA-World hypothesis hold that originally, RNA nucleotides were produced by purely chemical processes in the environment, and that life evolved from self-replicating RNA molecules made up from these abiotically-produced monomers. Later, life evolved a cellular metabolism by which it could construct its own RNA monomers. This satisfies point (2) because it says that the environment provided RNA rather than some other heteropolymer with catalytic properties; the evolutionary solution echoes the environmental one in that it uses the same complex molecule.
Wächterschäuser's Iron-Sulphur World theory, and many of its descendants, including Russel's alkaline vent theory, hold that the reductive tricarbolic acid cycle (rTCA cycle, aka reverse citric acid cycle) was originally catalysed by mineral surfaces. This enabled the formation of the first cells, which eventually evolved enzymes that could be used to catalyse the rTCA cycle without the mineral catalysts. This satisfies point (2) because it says that the first evolved solution used essentially the same chemical pathway as the one provided by the environment, just with different catalysts.
(Not all hypotheses in origins of life have this form. Some versions of the RNA World theory hold that RNA-based life was preceded by life based on some other heteropolymer, for example. But the hypotheses described above are very popular.)
From an evolutionary biology point of view, point (2) seems rather an odd feature for a hypothesis to have. Evolution is great at producing novel solutions to problems, but to my knowledge it isn't good at copying old ones. (Mimicry doesn't provide a counterexample to this, since it's about appearance rather than mechanism, and often the mimic produces the same visual effect through a very different mechanism. For example, although the treehopper Cyphonia clavata mimics the outward appearance of an ant, it does so not by being anatomically similar to an ant but by having a face on its butt.)
Consequently I'm looking for known examples from evolutionary biology that satisfy both point (1) and point (2). That is, I'm looking for examples where a species originally relied on some relatively complex process in its environment, and became less dependent on its environment by evolving a mechanism that closely echoes the one originally provided by the environment.
An example that might fit the bill would be a species that was originally unable to produce a key metabolite (e.g. an amino acid), but then later evolved the ability to produce the metabolite for itself. Evidence for this might be constituted by finding a species that produces the metabolite using a novel set of proteins, indicating that the capability to produce the metabolite was lost and then re-evolved. It would make an even better example if the novel proteins catalyse substantially the same chemical pathway that other species use to produce the same metabolite.
It may be that no good examples of this exist, which is actually better for me than if they do. More than any particular example, the main thing I want to know is whether ideas along these lines have been discussed in evolutionary biology at all (perhaps outside the context of the origins of life), and if so where I can find the literature on it.